Assigns QTL to a list of Haplotypes

Description

AssignQTL assigns QTL to the qtl of objects of class haplotype. ListQTL returns a list of qtl which for the object of class haploList.

Usage

AssignQTL(hList,nqtl = NA,frqtl = NA,sigma2qtl = NULL,shQTL = 1,scQTL = 1,
                      nTraits = 1,overlap = 0,MAF = 0.1,rmCausSNP =
TRUE)
ListQTL(hList,nqtl = NA,frqtl = NA,sigma2qtl = NULL,shQTL = 1,scQTL = 1,
                      nTraits = 1,overlap = 0,MAF = 0.1)

Arguments

Value

A list of length nHaplotpes.

See Also

SampleHaplotype

Examples

hList <- SampleHaplotypes(nHaplotypes = 20,nLoc = 100,genDist =
1,nDec = 3) ## create objects
 hListd <- SampleHaplotypes(orig = hList,genDist = 1,nDec = 3)
hListQTL <- AssignQTL(hList,frqtl = 0.1,MAF = 0.0)
hListd <- SampleHaplotypes(orig = hListQTL,genDist = 1,nDec
= 3,QTL = TRUE)
qtlList <- ListQTL(hList,frqtl = 0.1,MAF = 0.0)

Remove the homozygotic snp loci from a list of haplotypes

Description

Finds homozygotic marker loci in a list of haplotypes and removes these from all haplotypes.

Usage

RemoveHomozygotes(hList)

Arguments

Value

A list of objects of class haplotype.

See Also

SampleHaplotypes, SampleHaplotype.

Examples

hList <- SampleHaplotypes(nHaplotypes = 20,nLoc = 100,genDist =
1,nDec = 3) ## create objects
hList <- RemoveHomozygotes(hList)

Simulate a base population haplotype

Description

Simulates a base population haplotype.

Usage

SampleBaseHaplotype(genDist,nDec,nLoc,pSnp = seq(0,1,length.out = nLoc))

Arguments

Details

Generally called by function SampleHaplotypes.

Value

An object of class haplotype.

See Also

SampleHaplotypes, SampleBaseHaplotype

Examples

hList <- sapply(1:10,function(x)SampleBaseHaplotype(genDist = 1,nDec
= 2,nLoc = 50))

Simulate a haplotype

Description

Simulates a haplotype, either sampling using population parameters or through a meiosis event with two parental haplotypes.

Usage

SampleHaplotype(H0 = NULL,H1 = NULL,genDist,nDec,nChrom = 1,prMut =
1E-5,QTL = F,checkValidity = TRUE) 

Arguments

Details

Markers are continually spaced over the whole genome. Marker density is specified in SampleBaseHaplotype. Position of 1 alleles is recorded and stored in @snp attribute of the object of class haplotype. If QTL is TRUE, haplotypes with QTL's need to be provided. If not, nothing happens apart from mutations (same prob. as for single basepairs). Function SampleHaplotype is generally called by function SampleHaplotypes.

Value

An object of class haplotype.

See Also

SampleHaplotypes, SampleBaseHaplotype

Examples

hList <- SampleHaplotypes(nHaplotypes = 20,genDist =
1,nDec = 3,nLoc = 20) ## create objects
h <- SampleHaplotype(H0 = hList[[1]],H1 = hList[[2]],genDist =
1,nDec = 3)

Simulate a list of haplotypes

Description

Simulate a list of haplotypes, either sampling using population parameters or from a previous list of haplotypes through a series of meioses.

Usage

SampleHaplotypes(orig = NULL,nHaplotypes = 10,nMeioses = 2,gg = NULL,...)

Arguments

Details

The function SampleHaplotypes creates individuals by randomly combining haplotypes from the list. Meiosis events in individuals create new haplotypes. Argument nOff sets the number of meiosis events within each individual. Argument nHaplotypes has only effect when sampling a base population. See SampleBaseHaplotype for sampling base haplotypes and for arguments of this function.

Value

A list of length nHaplotpes or nOff * length(orig) of objects of class haplotype.

See Also

SampleHaplotype, SampleBaseHaplotype

Examples

hList <- SampleHaplotypes(nHaplotypes = 20,nLoc = 100,genDist =
1,nDec = 3) ## create objects
for(g in 1:10)hList <- SampleHaplotypes(orig = hList,genDist
= 1,nDec = 3)

Simulate a haplotypes in a pedigree

Description

Simulates haplotypes within a given pedigree. Haplotypes for a base individual are sampled from a list of base haplotypes. Parameters for sampling haplotypes are passed to function SampleHaplotype.

Usage

SamplePedigree(orig,ped,...)

Arguments

Details

Samples haplotypes for individuals in a pedigree and returns a pedigree with two additional columns which identify the two haplotypes of an individual together with a list of haplotypes. Uses function SampleHaplotype to sample a meiosis event between two parental haplotypes.

Value

A list with a pedigree and a list of objects of class haplotype.

See Also

SampleHaplotype, orderPed

Examples

example(SampleHaplotypes)
ID <- 1:10
pID0 <- c(rep(0,5),1,1,3,3,5)
pID1 <- c(rep(0,4),2,2,2,4,4,6)
ped <- data.frame(ID,pID0,pID1)
phList <- SamplePedigree(orig = hList,ped = ped)

Build a haplotype pedrigree from a haplotype list

Description

Builds a haplotype pedigree from a list of objects of class haplotype. Objects have attributes hID and phID0, phID1, the last two refer to the two haplotypes in the parent. Function can construct a new pedigree or continue a given pedigree. Simulate a list of haplotypes, either sampling using population parameters or from a previous list of haplotypes through a series of meioses.

Usage

buildhPedigree(hPedigree = NULL,hList)

Arguments

Details

The function buildhPedigree uses the attributes hID, phID0, phID1 of objects of class haplotype to build a pedigree of haplotypes. Each haplotype originates from a pair of parental haplotypes between which the meiosis event occured or has no known parental haplotypes.

Value

A data.frame.

See Also

SampleHaplotypes

Examples

example(SampleHaplotypes)
hPedigree <- buildhPedigree(hList = hList)
for(g in 1:10)
  {
    hList <- SampleHaplotypes(orig = hList,genDist
        = 1,roundDec = 3)
    hPedigree <- buildhPedigree(hPedigree=hPedigree,hList = hList)
  }

Get alleles

Description

Extract the sequence of snp alleles from a list of objects of class haplotype.

Usage

getAll(hList,what = c("snp","qtl"),removeHomozygotes =
FALSE,translatePos = TRUE)

Arguments

Details

Function removes homozygous snp loci before extracting these.

Value

Matrix.

Examples

example(AssignQTL)
hh <- getAll(hList = hList)
qq <- getAll(hList = hList,what = 'qtl')

Transform a haplotype pedigree into a pedigree.

Description

Transforms a haplotype pedigree into a pedigree. Individuals in a haplotype pedigree are identified through meiosis. The number of rows of the pedigree equals the number of unique combinations of haplotypes plus the number of haplotypes which did not 'participate' in a meiosis event. The latter haplotypes form individuals with only one haplotype and thus only one parent. Row number of the pedigree identifies individuals. The pedigree has four columns. Columns 3 and 4 identify the haplotypes of the individual. Columns 1 and 2 identify parental individuals of the individuals by their row number in the pedigree.

Usage

hPed2Ped(hPed)

Arguments

Value

A data.frame.

See Also

SampleHaplotype, buildhPedigree

Examples

example(buildhPedigree)
ped <- hPed2Ped(hPedigree)

Function to create objects of class 'haploList'

Description

Function to create objects of class 'haploList'. Can eiter copy the attributes of an earlier object of class 'haploList' or create a new 'haploList' object. Function mostly used within other functions.

Usage

haploList(list = NULL,hList = NULL,nDec,genDist,nChrom = 1)

Arguments

Value

An object of class 'haploList'. If list is not NULL, object of filled with objects of class 'haplotype'.

See Also

haplotype, haploList

Examples

hList <- haploList(nDec=  1,genDist = 1)
validhaploListObject(hList)

Class "haploList"

Description

Class definition of haploList. Extends lists to contian objects of class haplotype. Attributes are nDec, the number of decimal positions and genDist, the genome size measured in Morgan.

Objects from the Class

Objects can be created by calls of the form new("haploList", ...).

Slots

.Data:

Object of class "list" containing objects of class 'haplotype'

genDist:

Object of class "numeric" expressing the genome size in Morgan.

nDec:

Object of class "integer" expressing the number of decimal positions of the haplotypes.

nChrom:

Object of class "integer" expressing the number of chromosomes.

Extends

Class "list", from data part. Class "vector", by class "list", distance 2.

Methods

[

signature(x = "haploList", i = "ANY", j = "missing"): subset and extract from object of class 'haploList'

c

signature(x = "haploList"): concatenate object of class 'haploList'.

See Also

SampleHaplotypes, haplotype

Examples

showClass("haploList")

Class "haplotype" ~~~

Description

Definition of 'haplotype' class.

Objects from the Class

Objects can be created by calls of the form new("haplotype", ...).

Slots

snp:

Object of class "integer" containing the positions on the genome where the haplotype has a 1 allele. The number of snp positions is the genome size in Morgan times the number of decimal positions, both stored in 'haploList' objects.

qtl:

Object of class "list". Names of the list are the QTL positions, on the same scale as snp positions. Objects in the list are the QTL alleles.

hID:

Object of class "numeric" identifying the current object of class 'haplotype'.

phID0:

Object of class "numeric" pointing to the first parental haplotype.

phID1:

Object of class "numeric" pointing to the second parental haplotype.

Methods

No methods defined with class "haplotype" in the signature.

See Also

SampleHaplotype, SampleHaplotypes, haploList

Examples

showClass("haplotype") 

Function to validate an object of class 'haploList'

Description

Checks of object is of class 'haploList' and checks if all entries in object@.Data are of class 'haplotype'.

Usage

validhaploListObject(object)

Arguments

Value

Logical

See Also

haploList, haplotype